GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4440 - Domain of unknown function (DUF4440)
Pfam: PF14534 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0051
Length: 107
Sequences: 7447
Seq/Len: 69.6
HH_delta: 0.098 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
16_D19_A1.828753.738
21_A44_L1.314172.686
26_D40_K1.197662.448
75_G94_F1.15532.362
101_Q104_K1.11182.273
10_D14_A1.048962.144
77_W92_G1.038832.123
39_G42_A1.019582.084
28_F43_I1.00722.059
11_A19_A0.979792.003
4_L98_W0.971241.985
24_Y28_F0.906931.854
19_A22_S0.899741.839
17_I21_A0.893541.826
7_Q19_A0.858691.755
25_A101_Q0.794891.625
7_Q23_L0.778651.592
44_L48_K0.777231.589
21_A40_K0.766891.568
18_D44_L0.732841.498
72_V97_V0.719081.470
45_A49_S0.714181.460
3_A7_Q0.706781.445
70_T97_V0.693591.418
73_V98_W0.677781.385
41_E45_A0.674791.379
66_V71_A0.664421.358
58_K78_T0.643721.316
63_E74_R0.642381.313
8_Y20_L0.639881.308
78_T91_R0.625591.279
69_D100_K0.620791.269
11_A23_L0.614951.257
39_G43_I0.570561.166
64_V73_V0.56781.161
74_R95_T0.556521.138
41_E44_L0.556491.138
64_V71_A0.553261.131
6_E10_D0.548631.121
24_Y43_I0.542791.109
17_I48_K0.54271.109
62_V76_R0.540681.105
70_T99_K0.539641.103
42_A45_A0.536011.096
56_S80_T0.531861.087
18_D21_A0.527611.078
40_K44_L0.526171.076
43_I47_F0.525021.073
11_A16_D0.517731.058
8_Y12_F0.508331.039
5_E98_W0.507341.037
65_R72_V0.504581.031
9_E13_N0.50381.030
75_G96_S0.500551.023
60_E78_T0.495691.013
5_E96_S0.493461.009
8_Y23_L0.489781.001
76_R91_R0.488960.999
100_K104_K0.484630.991
69_D99_K0.482940.987
76_R93_R0.482650.987
45_A48_K0.473210.967
7_Q10_D0.457110.934
61_D76_R0.455170.930
12_F20_L0.45380.928
18_D22_S0.449280.918
78_T89_T0.442240.904
29_V38_L0.435920.891
38_L42_A0.427810.874
11_A22_S0.427770.874
67_L70_T0.425590.870
21_A41_E0.42260.864
20_L47_F0.419970.858
4_L7_Q0.417790.854
31_V36_T0.415630.850
14_A19_A0.407720.833
7_Q11_A0.405950.830
7_Q22_S0.400210.818
72_V95_T0.39830.814
4_L23_L0.390910.799
10_D13_N0.38980.797
60_E76_R0.388360.794
40_K43_I0.385970.789
67_L72_V0.383830.785
77_W96_S0.383320.784
25_A99_K0.383080.783
5_E73_V0.366390.749
80_T89_T0.364510.745
68_G71_A0.356870.729
16_D22_S0.352990.722
67_L97_V0.351190.718
22_S104_K0.347170.710
59_F75_G0.342670.700
15_G51_F0.338760.692
8_Y24_Y0.336790.688
5_E75_G0.335940.687
43_I46_A0.334140.683
6_E62_V0.333840.682
25_A40_K0.333730.682
77_W94_F0.332180.679
57_I79_F0.331590.678
9_E77_W0.327070.669
74_R93_R0.324960.664
30_F43_I0.32460.664
71_A100_K0.324160.663
33_P47_F0.323320.661
27_D101_Q0.322620.659
9_E59_F0.320470.655
24_Y40_K0.314570.643
69_D101_Q0.313740.641
17_I20_L0.31370.641
11_A14_A0.311520.637
75_G98_W0.309220.632
26_D101_Q0.308220.630
13_N56_S0.307940.629
75_G92_G0.307780.629
13_N59_F0.305230.624
62_V75_G0.302810.619
31_V35_G0.29660.606
56_S78_T0.29470.602
5_E9_E0.291350.596
65_R99_K0.290070.593
55_S82_R0.289430.592
77_W81_W0.288040.589
32_G94_F0.286980.587
25_A28_F0.285470.584
6_E9_E0.284950.582
26_D41_E0.284120.581
30_F75_G0.280650.574
8_Y47_F0.278610.569
30_F50_G0.277220.567
18_D48_K0.276770.566
3_A6_E0.275730.564
46_A57_I0.275290.563
82_R85_G0.274970.562
20_L23_L0.274270.561
65_R74_R0.27330.559
48_K52_A0.271330.555
13_N58_K0.269980.552
9_E12_F0.268280.548
28_F32_G0.268070.548
51_F57_I0.26730.546
17_I51_F0.266740.545
37_I42_A0.266660.545
12_F94_F0.266530.545
77_W90_I0.266510.545
5_E8_Y0.266430.545
13_N57_I0.265860.543
28_F40_K0.262840.537
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3robA199.40.098
2gxfA199.40.105
3hx8A199.40.106
3bb9A199.30.123
3h51A199.30.137
3d9rA199.30.138
3fsdA199.30.14
3f7sA0.990799.30.161
3gwrA0.990799.20.172
2r4iA199.20.173

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